Abstract 3379: Comprehensive circulating tumor DNA and CTC profiling of treatment naïve early-stage head and neck cancer patients reveals early signature of disease progression
Authors: Gowhar Shafi, Atul Bharde, Fauzul Moubeen, Kanchan Hariramani, Alain D’Souza, Trupti Kad, Bhagwat Jadhav, Sangita Prajapati, Aditi Rani, Madhura Basavalingegowda, Mohan Uttarwar, Gourishankar Aland, Sreeja Jayant, Aravindan Vasudevan, Pankaj Chaturvedi, Jayant Khandare
Journal: Cancer Research (2023)

Abstract Comprehensive CtDNA and CTC profiling of treatment naïve early-stage head and neck cancer patients reveals early signatures of disease progressionBackground: We performed comprehensive ctDNA analysis on early-stage HNC patients in a pilot study to determine the mutational landscape in HNC patients with a known tobacco history. Methods: We analysed ctDNA of 18 early-stage HNC patients for genomic landscapes using the illumina NextSeq 2000 NGS. A custom-designed OncoIndex gene panel was used for the hybrid capture target-enrichment of critical cancer genes. Panel was designed to detect cancer targeting exonic sequence of 600 genes reporting SNVs and indels along fusions and copy number amplification. The gene panel detected genome-wide signatures including bTMB, MSI (microsatellite instability), HRD (homologous recombination deficiency) prediction and calculate cfDNA tumor fraction. Results: 80 % patients showed presence of at least one CTC in peripheral blood, possibly indicating the progressive disease at the time of presentation. Comprehensive genomic profile obtained from plasma cfDNA of early-stage HNC cancer patients predominantly had low bTMB and MSI Scores (99 % patients). However, HRD and LOH matrix was high for 60 % patients indicating highly dysregulated DNA repair activities. Concurring to these observations, 98 % patients had mutations in key tumor suppressor and DNA damage response (DDR) genes possibly resulting in their loss of function. Besides DNA damage pathway, 60% patients harboured alterations in RTK genes including FGFR, EGFR and PDEGFR family and 32% patients showed activating mutations in Erk1 and its upstream regulators. MSH2 was the most prominently mutated gene (37%) followed by FGFR (32%). Surprisingly, unlike HPV positive advanced HNC cases, TP53 mutations were not detected in any patient, though alterations in TS genes were most prevalent in the study population. 51% alterations resulted into truncated proteins possibly impairing their functions, while 42% alterations were point mutations, 6 % were frameshift and 1 % indels. Presence of mutations in BRAF, PDGFR, FGFR and KIT genes suggested for the potential therapy resistance. Tumor fraction representing ctDNA showed elevated range from 20 % to 45 % with a corresponding ploidy between 2 to 4. Conclusions: Comprehensive ctDNA profile showed major gene alterations in TS and DDR response pathway genes besides mutations in proliferative signaling members. TP53 mutation was not detected, although critical tumor suppressor and DDR genes were predominantly mutated, suggesting for a unique mutation pattern associated with early-stage HNC due to tobacco etiology. Our results suggest that comprehensive ctDNA analysis along CTC profiling can predict the disease progression beforehand and may offer new treatment options to early-stage HNC patients. Citation Format: Gowhar Shafi, Atul Bharde, Fauzul Moubeen, Kanchan Hariramani, Alain D’Souza, Trupti Kad, Bhagwat Jadhav, Sangita Prajapati, Aditi Rani, Madhura Basavalingegowda, Mohan Uttarwar, Gourishankar Aland, Sreeja Jayant, Aravindan Vasudevan, Pankaj Chaturvedi, Jayant Khandare. Comprehensive circulating tumor DNA and CTC profiling of treatment naïve early-stage head and neck cancer patients reveals early signature of disease progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3379.